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graph TD;
    A[Start] --> B[Find and annotate gene locations using DNA Master]
    B --> C{Inspect Glimmer and Genemark reports}
    C -->|Yes| D[Obtain RBS score]
    D --> E[Compare ORFs with Starterator]
    E --> F{Obtain gene functions}
    F -->|Yes| G[Cross-check against genes with known functions]
    G --> H[Annotate results]
    F -->|No| H1[Use BLAST-NCBI, HHPred, BLAST-phagesDB to deduce possible gene functions]
    H1 --> G
    C -->|No| I[Iterate through next gene]
    I --> C
    D -->|No| I
    I --> D
    H --> J[Confirm tRNA locations using ARAGORN and tRNAscan-SE]
    J --> K[Search for slippery sequences within translation frameshift regions]
    K --> L[Annotate results]
    L --> M[End]

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